During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced in non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focussing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridisation. Using RAD sequencing (27 611 SNPs), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, stressing their ability to interbreed and the potential threat they cause to the genetic integrity of native tilapias. Populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity with Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge to avoid introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.

Variant Call Format (vcf) file with genotypes and allele depths of all tilapia specimens. Only bi-allelic variable sites that had a mapping quality higher than 30 and that were called in at least 80% of all specimens were included. Afterwards one SNP per RADtag was randomly selected and sites characterized by heterozygosity excess (q-value <0.05) were subsequently discarded.